nf-core / pangenome

Related projects ⓘ

Alternatives and complementary repositories for pangenome

• PacificBiosciences / HiPhase
  Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
  ☆70Updated last month
• TimD1 / vcfdist
  vcfdist: Accurately benchmarking phased variant calls
  ☆76Updated last week
• gatech-genemark / ProtHint
  Protein hint generation pipeline for gene finding in eukaryotic genomes
  ☆56Updated last year
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆102Updated this week
• marschall-lab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆85Updated 2 weeks ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆65Updated last week
• clemgoub / TE-Aid
  Annotation helper tool for the manual curation of transposable element consensus sequences
  ☆44Updated 5 months ago
• santiagosnchez / vcf2fasta
  Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file
  ☆46Updated last month
• arangrhie / merfin
  Evaluate variant calls and its combination with k-mer multiplicity
  ☆63Updated last year
• Gabaldonlab / perSVade
  perSVade: personalized Structural Variation detection
  ☆36Updated 4 months ago
• epi2me-labs / pychopper
  cDNA read preprocessing
  ☆61Updated 3 months ago
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆71Updated 5 months ago
• bcgsc / straglr
  Tandem repeat expansion detection or genotyping from long-read alignments
  ☆67Updated last month
• GeneDx / pgr-tk
  PGR-TK: Pangenome Research Tool Kit
  ☆93Updated 6 months ago
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆174Updated 3 months ago
• epi2me-labs / wf-alignment
  ☆23Updated this week
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆105Updated last month
• arangrhie / T2T-Polish
  Evaluation and polishing workflows for T2T genome assemblies
  ☆104Updated 3 weeks ago
• marbl / ModDotPlot
  ☆119Updated last month
• lh3 / dipcall
  Reference-based variant calling pipeline for a pair of phased haplotype assemblies
  ☆96Updated 3 years ago
• eblerjana / pangenie
  Pangenome-based genome inference
  ☆111Updated this week
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆103Updated 4 months ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆108Updated last month
• nadegeguiglielmoni / genome_assembly_tools
  List of genome assembly tools
  ☆51Updated last week
• EVidenceModeler / EVidenceModeler
  source code for EVM
  ☆103Updated 10 months ago
• nanoporetech / katuali
  Analysis pipelines from Oxford Nanopore Technologies' Research Division
  ☆50Updated 4 years ago
• KolmogorovLab / hapdup
  Pipeline to convert a haploid assembly into diploid
  ☆90Updated 5 months ago
• WGLab / NanoCaller
  Variant calling tool for long-read sequencing data
  ☆100Updated 5 months ago
• bcgsc / ntSynt
  Detecting multi-genome synteny using minimizer graph mapping
  ☆70Updated last week
• eldariont / svim-asm
  Structural Variant Identification Method using Genome Assemblies
  ☆93Updated 2 years ago